Abstract: Sea transportation is very important and strategic for Indonesia. It is because Indonesia is an archipelagic country with most of its coverage is sea. Therefore, sea is very important in connectivity among islands. One entity in sea connectivity is port. Indonesia has 25 strategic ports that are spread from Sumatera in the West and Papua in the East. One method to analyze the sea transportation activity is by analyzing the ports activity. In this research, we observe and analyze the activity of these 25 strategic ports in Indonesia. Rather than manually, we use computational technology by using clustering method. In this researcher, we use agglomerative clustering method which it is a part of hierarchical clustering method that use bottom-up approach. The port activity parameters that are observed include: cargo loading and unloading, ship call and passenger arrival and departure. We use 2017 data that was published by central bureau of statistics of Indonesia in late of 2018. There are several findings through this research. First, there is significant disparity among strategic ports which is most of them are at low performance or activity. Second, the ports activities strengthen argument that export commodities of Indonesia are dominated by natural resources and raw materials. In the other side, import commodities of Indonesia are dominated by end or cosumer products. Most of industrial products that are supplied by local industry are used to fulfill domestic demand. In passenger activitiy, Batam becomes the most strategic connection between Sumatera, Singapore and Johor.